Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_007694083.1 C447_RS11620 class II fructose-bisphosphate aldolase
Query= BRENDA::D4GYE0 (330 letters) >NCBI__GCF_000336675.1:WP_007694083.1 Length = 336 Score = 301 bits (770), Expect = 2e-86 Identities = 153/326 (46%), Positives = 221/326 (67%), Gaps = 8/326 (2%) Query: 8 ELATVYDEALDEGFGLIASNIAEPNIMMGLMEGADRMDSDLLLQMSGGACRFAGDGDAVA 67 +L +Y+ A +G ASN+ + ++++GL++G+ D+DL++Q S F G GD Sbjct: 10 DLRELYERARAGRYGFFASNVTQFDVLVGLLDGSAAADADLVVQASREEAAFFGGGDPTV 69 Query: 68 GLKAMGNYIETIAERYDIGVFLNMDH---QTDLEFIEQQIELDIPSSIMIDASHEPFDEN 124 GL+ +G ++++A+RY I F N+DH + F+E ++ D+P S+M+DAS PF+EN Sbjct: 70 GLEVLGAALDSLADRYGIEAFCNVDHVHLPEEQSFLETCLDSDVPDSVMVDASDRPFEEN 129 Query: 125 VATSREVVEMVEAAGSDVLIEAELGQIKGVEDEIE--AEEAFYTDPEQAVEFVDKTGADL 182 V + E VE A DVL+EAELG+I GVE E A+EAFYTDP AVEFV++TG DL Sbjct: 130 VELTAETVER---ADDDVLVEAELGRIAGVEGSTETAADEAFYTDPGTAVEFVERTGCDL 186 Query: 183 LAISVGTQHGVAKGKDLELRPDLANDIRQALRDHGLDTPLVLHGSSGVQPDQLQEMLKHG 242 LA+S+GTQHGVA +DL++RPDLA I +AL + G +T LV+HG+SG+ ++++ +L G Sbjct: 187 LAVSIGTQHGVASDRDLDVRPDLAVAIDEALVEAGEETFLVVHGASGLADERIEALLDAG 246 Query: 243 ICKVNKDTRYQYEYTRTAYDRYNEEPNAIVPPEGVADARDTFFNETDWSPNKDVFDPRVA 302 +CK NK+TRYQYE+ RTA D Y++ +AI PPEGV D R FF +DWSP K F P V Sbjct: 247 VCKFNKNTRYQYEFARTAADFYHDHADAIRPPEGVPDDRSNFFAGSDWSPEKASFHPHVV 306 Query: 303 GRDIRERIADVHADLTEVSGSAGQSL 328 R RIA V ++L EV+G+AG+++ Sbjct: 307 SNAARNRIATVMSELCEVTGNAGETM 332 Lambda K H 0.315 0.135 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 390 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 330 Length of database: 336 Length adjustment: 28 Effective length of query: 302 Effective length of database: 308 Effective search space: 93016 Effective search space used: 93016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory